Although dogs with floppy ears tend to be more prone to infection, Boston Terrier ears, which are upright, may also develop problems. Good basic dog ear care will be all most dogs need.
However, allergies, food, inhalants and hormonal problems (e.g., hypothyroidism) can sometimes contribute to infection. If your dog has recurring problems, you will need to seek out the underlying cause in order to cure it.
Water is a haven for bacteria growth. If water does accidentally get in, use a drying agent. A mixture of equal parts hydrogen peroxide (3% solution) and 70% rubbing alcohol can be used. A substitute is equal parts white vinegar and water. Your veterinarian can also recommend suitable products for ear cleaning.
Use cotton-tip swabs carefully when cleaning. They may pack debris in rather than removing it. A good rule of thumb is to only clean what you can see.

If your Boston has recurring infections, your veterinarian may recommend sedating and flushing, perhaps multiple times, to get the area clean enough for medication to make contact and be effective. Chronic cases of infection may warrant thyroid testing and/or a hypoallergenic diet for a trial period (10 to 12 weeks). A dermatologist may also be seen for consultation.
If you think your Boston has a problem, contact your veterinarian right away to avoid complications, even surgery. These problems can quickly become serious.